Provenance in bioinformatics workflows

In this work, we used the PROV-DM model to manage data provenance in workflows of genome projects. This provenance model allows the storage of details of one workflow execution, e.g., raw and produced data and computational tools, their versions and parameters. Using this model, biologists can access details of one particular execution of a workflow, compare results produced by different executions, and plan new experiments more efficiently. In addition to this, a provenance simulator was created, which facilitates the inclusion of provenance data of one genome project workflow execution. Finally, we discuss one case study, which aims to identify genes involved in specific metabolic pathways of Bacillus cereus, as well as to compare this isolate with other phylogenetic related bacteria from the Bacillus group. B. cereus is an extremophilic bacteria, collectemd in warm water in the Midwestern Region of Brazil, its DNA samples having been sequenced with an NGS machine

Imaging features of discospondylitis in cats

ObjectivesThis study describes the imaging features of feline discospondylitis on MRI, comparing them to CT and radiographic findings where available.MethodsThe medical records of cats diagnosed with discospondylitis, presented to three referring institutions, were reviewed. MRI, CT and radiographic features were assessed by two of the authors independently.ResultsFourteen sites of discospondylitis were retrospectively identified in 13 cats. The L7–S1 intervertebral disc space (IVDS) was affected in 7/14 (50%) cases. Characteristic MRI features included a hyperintense nucleus pulposus signal on T2-weighted (T2W) imaging (n = 10/14 [71%]) and short tau inversion recovery (STIR) imaging (n = 11/13 [85%]), with contrast enhancement in all (n = 11/11); involvement of adjacent vertebral endplates (n = 11/14 [79%]) and hyperintense neighbouring soft tissue on T2W (n = 11/14 [79%]) and STIR (n = 10/13 [77%]), with contrast enhancement in all (n = 11/11); and the presence of spondylosis deformans (n = 10/14 [71%]). Other features included narrowed or collapsed IVDS (n = 8/14 [57%]), contrast enhancement of vertebral bodies (n = 5/11 [46%]), epidural space involvement (n = 5/14 [36%]), compression of the spinal cord or nerve roots (n = 5/14 [36%]), paraspinal abscessation (n = 3/14 [21%]) and meningeal signal intensity abnormalities with contrast enhancement (n = 5/6 [83%]). These latter findings may indicate secondary focal meningitis. Radiographs were available covering five sites (in four cats) and CT covering three sites (in two cats). The most common radiological features were collapse or narrowing of the affected IVDS (80%) and endplate erosion (60%). No changes suggestive of discospondylitis were identifiable on radiography or CT in two sites (one cat), despite being identifiable on MRI. Repeated radiography in one case did not reveal complete radiological resolution following 9 months of treatment.Conclusions and relevanceThe results of this study indicate consistent MRI features of feline discospondylitis that should be considered in the diagnosis of this condition

Physical Exercise Restores the Generation of New born Neurons in an Animal Model of Chronic Epilepsy

Neurogenesis impairment is associated with the chronic phase of the epilepsy in humans and also observed in animal models. Recent studies with animal models have shown that physical exercise is capable of improving neurogenesis in adult subjects, alleviating cognitive impairment and depression. Here, we show that there is a reduction in the generation of newborn granule cells in the dentate gyrus of adult rats subjected to a chronic model of epilepsy during the postnatal period of brain development. We also show that the physical exercise was capable to restore the number of newborn granule cells in this animals to the level observed in the control group. Notably, a larger number of newborn granule cells exhibiting morphological characteristics indicative of correct targeting into the hippocampal circuitry and the absence of basal dendrite projections was also observed in the epileptic animals subjected to physical exercise compared to the epileptic animals. The results described here could represent a positive interference of the physical exercise on the neurogenesis process in subjects with chronic epilepsy. The results may also help to reinterpret the benefits of the physical exercise in alleviating symptoms of depression and cognitive dysfunction.Fapemig (Fundacao de Amparo a Pesquisa do Estado de Minas Gerais)CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico)FAPESP (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo)INNT (Instituto Nacional de Neurociencia Translacional)CAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior)Univ Fed Sao Joao del Rei, Dept Engn Biossistemas, Lab Neurociencia Expt Computac, Sao Joao Del Rei, BrazilHosp Israelita Albert Einstein, Inst Cerebro, Sao Paulo, BrazilUniv Mogi das Cruzes, Nucleo Pesquisas Tecnol, Mogi Das Cruzes, BrazilUniv Fed Sao Paulo UNIFESP, Dept Fisiol, Escola Paulista Med, Sao Paulo, BrazilUniv Fed Sao Paulo UNIFESP, Disciplina Neurol Expt, Escola Paulista Med, Sao Paulo, BrazilUniv Fed Sao Paulo UNIFESP, Dept Fisiol, Escola Paulista Med, Sao Paulo, BrazilUniv Fed Sao Paulo UNIFESP, Disciplina Neurol Expt, Escola Paulista Med, Sao Paulo, BrazilWeb of Scienc

Association of magnetic resonance assessed disc degeneration and late clinical recurrence in dogs treated surgically for thoracolumbar intervertebral disc extrusions

BackgroundRadiographic signs of intervertebral disc mineralization are thought to indicate sites of future recurrence of disc extrusion (Hansen type I) but the relationship between evidence of disc degeneration on magnetic resonance imaging (MRI) and future disc extrusion with recurrence of clinical signs has not been examined.ObjectivesTo examine the relationship between MRI-assessed degeneration of thoracolumbar intervertebral discs and late recurrence of clinical signs in dogs presented with acute thoracolumbar intervertebral disc extrusion and treated by hemilaminectomy alone.AnimalsNinety-two client-owned dogs presented to 2 referral hospitals between 2009 and 2014.MethodsRetrospective analysis of association between clinical signs consistent with recurrent thoracolumbar intervertebral disc extrusion and MRI evidence of disc degeneration in dogs undergoing hemilaminectomy for acute thoracolumbar intervertebral disc extrusion. Univariable and multivariable Cox regression analyses were used to explore associations between recurrence of clinical signs and several characteristics of T10-L3 discs at initial diagnosis.ResultsNinety-two cases were included, of which 42 (46%) were Dachshunds and median age was 5.3 years. Clinical signs recurred in 33/92 (36%) dogs. Finding a completely degenerate disc in the T10 to L3 region (in addition to the operated site) at the time of surgery was associated with a hazard ratio of 2.92 (95% confidence interval: 1.37-6.20) for recurrence of clinical signs.Conclusions and clinical importanceOur results suggest that in cases of thoracolumbar intervertebral disc extrusion in dogs, recurrence of signs is likely if at least 1 completely degenerate disc in addition to the currently symptomatic disc is visible on MRI

Chronic Sleep Restriction during Pregnancy - Repercussion on Cardiovascular and Renal Functioning of Male Offspring

Changes in the maternal environment can induce fetal adaptations that result in the progression of chronic diseases in the offspring. the objective of the present study was to evaluate the effects of maternal chronic sleep restriction on blood pressure, renal function and cardiac baroreflex response on male offspring at adult age. Female 3-month-old Wistar rats were divided in two experimental groups: control (C) and chronic sleep restricted (CSR). Pregnancy was confirmed by vaginal smear. Chronic sleep restricted females were subjected to sleep restriction by the multiple platform technique for 20 h daily, between the 1st and 20th day of pregnancy. After birth, the litters were reduced to 6 rats per mother, and were designated as offspring from control (OC) and offspring from chronic sleep restricted (OCSR). Indirect blood pressure (BPi tail cuff) was measured by plethysmography in male offspring at 3 months old. Following, the renal function and cardiac baroreflex response were analyzed. Values of BPi in OCSR were significantly higher compared to OC [OC: 127 +/- 2.6 (19); OCSR: 144 +/- 2.5 (17) mmHg]. the baroreflex sensitivity to the increase of blood pressure was reduced in OCSR [Slope: OC: -2.6 +/- 0.15 (9); OCRS: -1.6 +/- 0.13 (9)]. Hypothalamic activity of ACE2 was significantly reduced in OCSR compared to OC [OC: 97.4 +/- 15 (18); OSR: 60.2 +/- 3.6 (16) UAF/min/protein mg]. Renal function alteration was noticed by the increase in glomerular filtration rate (GFR) observed in OCSR [OC: 6.4 +/- 0.2 (10); OCSR: 7.4 +/- 0.3 (7)]. Chronic sleep restriction during pregnancy caused in the offspring hypertension, altered cardiac baroreflex response, reduced ACE-2 activity in the hypothalamus and renal alterations. Our data suggest that the reduction of sleeping time along the pregnancy is able to modify maternal homeostasis leading to functional alterations in offspring.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Associacao Fundo de Incentivo a Pesquisa (AFIP)Universidade Federal de São Paulo, Dept Fisiol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Psicobiol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Biociencias, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Fisiol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Psicobiol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Biociencias, São Paulo, BrazilFAPESP: FAPESP-10/51665-4Web of Scienc

Estimating cardiovascular risk in patients with type 2 diabetes: a national multicenter study in Brazil

According to Brazilian National Data Survey diabetes is the fifth cause for hospitalization and is one of the ten major causes of mortality in this country.Aimsto stratify the estimated cardiovascular risk (eCVR) in a population of type 2 diabetics (T2DM) according to the Framingham prediction equations as well as to determine the association between eCVR with metabolic and clinical control of the disease.MethodsFrom 2000 to 2001 a cross-sectional multicenter study was conducted in 13 public out-patients diabetes/endocrinology clinics from 8 Brazilian cities. the 10-year risk of developing coronary heart disease (CHD) was estimated by the prediction equations described by Wilson et al (Circulation 1998). LDL equations were preferably used; when patients missed LDL data we used total cholesterol equations instead.ResultsData from 1382 patients (59.0% female) were analyzed. Median and inter-quartile range (IQ) of age and duration of diabetes were 57.4 (51-65) and 8.8 (3-13) years, respectively without differences according to the gender. Forty-two percent of these patients were overweight and 35.4% were obese (the prevalence of higher BMI and obesity in this T2DM group was significantly higher in women than in men; p 20%) in 738 (53.4%), intermediate in 202 (14.6%) and low in 442 (32%) patients. Men [25.1(15.4-37.3)] showed a higher eCVR than women [18.8 (12.4-27.9) p < 0.001]. the most common risk factor was high LDL-cholesterol (80.8%), most frequently found in women than in men (p = 0.01). the median of risk factors present was three (2-4) without gender differences. Overall we observed that 60 (4.3%) of our patients had none, 154(11.1%) one, 310 (22.4%) two, 385 (27.9%) three, 300 (21.7%) four, 149 (10.5%) five and six, (2%) six risk factors. A higher eCVR was noted in overweight or obese patients (p = 0.01 for both groups). No association was found between eCVR with age or a specific type of diabetes treatment. A correlation was found between eCVR and duration of diabetes (p < 0.001), BMI (p < 0.001), creatinine (p < 0.001) and triglycerides levels (p < 0.001) but it was not found with HbA1c, fasting blood glucose and postprandial glucose. A higher eCVR was observed in patients with retinopathy (p < 0.001) and a tendency in patients with microalbuminuria (p = 0.06). Conclusion: our study showed that in this group of Brazilian T2DM the eCVR was correlated with the lipid profile and it was higher in patients with microvascular chronic complications. No correlation was found with glycemic control parameters. These data could explain the failure of intensive glycemic control programs aiming to reduce cardiovascular events observed in some studies.Univ Estado Rio de Janeiro, Diabet Unit, Rio de Janeiro, BrazilUniv São Paulo Scholl Med, Hosp Clin, Lab Clin & Expt Gatroenterol LIM07, São Paulo, BrazilUniv Fed Maranhao, Div Endocrinol, Sao Luis, BrazilUniv Estadual Campinas, Div Endocrinol, Campinas, BrazilCtr Estudos Diabet & Endocrinol Estado Bahia CEDE, Salvador, BA, BrazilUniv Fed Parana, Div Endocrinol, BR-80060000 Curitiba, Parana, BrazilHosp Agamenon Magalhaes, Div Endocrinol, Recife, PE, BrazilPosto Assistencia Med Jaguribe, Joao Pessoa, Paraiba, BrazilSanta Casa Porto Alegre, Div Endocrinol, Porto Alegre, RS, BrazilInst Assistencia & Previdencia Servidor Estado Ba, Div Endocrinol, Salvador, BA, BrazilSanta Casa Belo Horizonte, Diabet Unit, Belo Horizonte, MG, BrazilHosp Geral Goiania, Div Endocrinol, Goiania, Go, BrazilSecretaria Municipal Saude Brasilia, Brasilia, DF, BrazilUniversidade Federal de São Paulo, Div Endocrinol, São Paulo, BrazilUniversidade Federal de São Paulo, Div Endocrinol, São Paulo, BrazilWeb of Scienc

Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

<p>Abstract</p> <p>Background</p> <p>Hepatitis B virus (HBV) isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil.</p> <p>Results</p> <p>Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%), and most of these isolates were classified as subgenotype A1 (138/153; 90.2%). Genotype D was the most common genotype in the South (84.2%) and Central (47.6%) regions. The prevalence of genotype F was low (13%) countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5%) belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was <it>adw4</it>. The remaining isolate showed a leucine-to-isoleucine substitution at position 127.</p> <p>Conclusion</p> <p>The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin) indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F isolates belonged to cluster II, the presence of some isolates belonging to clusters I (subgroup Ib) and IV suggests the existence of two or more founder viral populations of genotype F in Brazil.</p

Nationwide multicenter study on the prevalence of overweight and obesity in type 2 diabetes mellitus in the Brazilian population

AIM: To evaluate the prevalence of overweight and obesity in type 2 diabetic (DM2) outpatients from different regions of Brazil. PATIENTS AND METHODS: We studied 2,519 randomly selected patients, from 11 hospitals, 2 endocrine and one general public care clinics from 10 cities. Overweight was defined as body-mass index (BMI) > 25 and obesity as BMI > 30 kg/m². Glycemic control (GC) was evaluated by GC index (GCI= patient's HbA1 or HbA1c/upper limit of normal for the method x 100). RESULTS: 39% of the population studied was male, the mean age was 58.8 ± 11.6 y, the duration from clinical diagnosis of DM2 was 9.0 ± 7.3y, and BMI was 28.3 ± 5.2 kg/m². No measurements of BMI were recorded from 265 patients (10.5%). Patients from the Northeast presented lower BMI as compared with those from the Midwest, Southeast and South areas, respectively (26.4 ± 4.7 vs. 27.9 ± 4.8 vs. 29.2 ± 5.1 vs. 29.4 ± 5.4 kg/m²; p 25 e obesidade um IMC > 30 kg/m². O controle glicêmico (CG) foi avaliado pelo índice de CG [ICG= HbA1 e ou HbA1c do paciente/limite superior de normalidade do método x 100]. RESULTADOS: Os pacientes tinham idade de 58,8 ± 11,6 anos, tempo de diagnóstico clínico de DM de 9,0 ± 7,3 anos, IMC de 28,3 ± 5,2 kg/m², e 39% eram do sexo masculino. Do total da amostra, 265 pacientes (10,5%) não apresentavam avaliação do IMC. Os pacientes da região Nordeste apresentaram menor IMC em comparação com os das regiões Centro-Oeste, Sudeste e Sul, respectivamente (26,4 ± 4,7 vs. 27,9 ± 4,8 vs. 29,2 ± 5,1 vs. 29,4 ± 5,4 kg/m²; p< 0,001). Houve maior prevalência de obesidade na região Sudeste e Sul em comparação à região Nordeste (p< 0,001) e nos pacientes do sexo feminino, respectivamente (69 vs. 31%; p< 0,001). Os pacientes com peso normal apresentaram menor ICG. Aqueles em tratamento com associação de duas ou mais drogas orais e associação de insulina + droga oral apresentaram maior IMC do que aqueles em tratamento com dieta, hipoglicemiante oral e insulina; p< 0,001. O IMC não diferiu entre os pacientes assistidos ou não por especialistas. CONCLUSÕES: Da população estudada, 75% não estava na faixa de peso ideal, sendo que um terço tinha obesidade. Nossos dados indicam que o sobrepeso e a obesidade já atingem um percentual de pacientes com DM2 no Brasil semelhante ao relatado em estudos europeus, mas ainda menor do que o observado nos EUA. A prevalência de obesidade nos pacientes diabéticos foi três vezes maior do que a observada na população brasileira em geral de acordo com os dados do IBGE.UERJUSPUNIFESP-EPMUNICAMPUNIFEUniversidade Federal do MaranhãoCEDEBVA Serviço de Endocrinologia e DiabetesHospital Agamenon Magalhães Serviços de EndocrinologiaSanta Casa Serviços de EndocrinologiaIAPSEB Serviços de EndocrinologiaHospital Geral Serviços de EndocrinologiaPAM Jaguaribe Serviços de EndocrinologiaSanta Casa Serviço de DiabetesSecretaria Municipal de SaúdeUNIFESP, EPMSciEL

Magnetic resonance imaging pattern recognition of metabolic and neurodegenerative encephalopathies in dogs and cats.

Metabolic/neurodegenerative encephalopathies encompass a wide list of conditions that share similar clinical and magnetic resonance imaging (MRI) characteristics, challenging the diagnostic process and resulting in numerous tests performed in order to reach a definitive diagnosis. The aims of this multicentric, retrospective and descriptive study are: (I) to describe the MRI features of dogs and cats with metabolic/neurodegenerative encephalopathies; (II) to attempt an MRI recognition pattern classifying these conditions according to the involvement of grey matter, white matter or both; and (III) to correlate the MRI findings with previous literature. A total of 100 cases were recruited, comprising 81 dogs and 19 cats. These included hepatic encephalopathy (20 dogs and three cats), myelinolysis (five dogs), intoxications (seven dogs and one cat), thiamine deficiency (two dogs and seven cats), hypertensive encephalopathy (three dogs and two cats), neuronal ceroid lipofuscinosis (11 dogs and one cat), gangliosidosis (three dogs and two cats), fucosidosis (one dog), L-2-hydroxyglutaric aciduria (13 dogs and one cat), Lafora disease (11 dogs), spongiform leukoencephalomyelopathy (one dog) and cerebellar cortical degeneration (four dogs and two cats). None of the hepatic encephalopathies showed the previously described T1-weighted hyperintensity of the lentiform nuclei. Instead, there was involvement of the cerebellar nuclei (8/23), which is a feature not previously described. Dogs with myelinolysis showed novel involvement of a specific white matter structure, the superior longitudinal fasciculus (5/5). Thiamine deficiency affected numerous deep grey nuclei with novel involvement of the oculomotor nuclei (3/9), thalamic nuclei, subthalamus and cerebellar nuclei (1/9). Cats with hypertensive encephalopathy had a more extensive distribution of the white matter changes when compared to dogs, extending from the parietal and occipital lobes into the frontal lobes with associated mass effect and increased brain volume. Lysosomal storage disease showed white matter involvement only, with neuronal ceroid lipofuscinosis characterised by severe brain atrophy when compared to gangliosidosis and fucosidosis. All patients with L-2-hydroxyglutaric aciduria had a characteristic T2-weighted hyperintense swelling of the cerebral and cerebellar cortical grey matter, resulting in increased brain volume. Lafora disease cases showed either normal brain morphology (5/11) or mild brain atrophy (6/11). Dogs with cerebellar cortical degeneration had more marked cerebellar atrophy when compared to cats. This study shows the important role of MRI in distinguishing different metabolic/neurodegenerative encephalopathies according to specific imaging characteristics